Illumina HiSeq 1500 paired end sequencing; Illumina paired end sequencing
Control tumor organoid
Five hundred fifty nanograms of genomic DNA were input for library preparation after fragmentation by Covaris S2, following the KAPA Hyper Prep Kit (KR0961-V1.14) protocols, with selection for a library size range of 250-450 bp. Three hundred nanograms per library DNA each from 12 samples were normalized and combined into a single pool for exome capture using the xGen Lockdown Probes and Reagents based on their standard protocols. Captured libraries were sequenced using the HiSeq1500 with paired end 101bp reads. Sequence reads were aligned to human genome build 37 (hg19) by BWA (version 0.7.10) and samtools (version 0.1.19). Duplicated reads were removed from the BAM files using Picard (version 1.73). These BAM files were recalibrated by Genome Analysis Toolkits (version 3.2-2) with default parameters.